# HG changeset patch
# User ric
# Date 1474547875 14400
# Node ID 5ceb7668e2591216aca25a418bfd439102db2ef7
# Parent  8fdf5996c0fb71788e9e7d31a28c8636e7245ade
Deleted selected files

diff -r 8fdf5996c0fb -r 5ceb7668e259 boh/importer.py
--- a/boh/importer.py	Thu Sep 22 08:37:42 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# BEGIN_COPYRIGHT
-# END_COPYRIGHT
-
-import sys
-from bl.vl.app.importer.main import main
-
-main(sys.argv[1:])
diff -r 8fdf5996c0fb -r 5ceb7668e259 boh/individual.xml
--- a/boh/individual.xml	Thu Sep 22 08:37:42 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-<tool id="vl_import_individual" name="VLI.individual">
-  <description>import individual definitions within omero/vl</description>
-  <command interpreter="python">
-    #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py
-    #else #unauthorized_access.py
-    #end if
-    #if $advanced_configuration.configuration_level == 'advanced'
-      --host=$advanced_configuration.vl_host
-      --user=$advanced_configuration.vl_user
-      --passwd=$advanced_configuration.vl_passwd
-    #end if
-    --operator=galaxy
-    --ifile=$input
-    --ofile=$output
-    --report_file=$report
-    --loglevel=$__app__.config.vl_loglevel
-    --logfile=$logfile
-    #if $blocking_validation
-      --blocking-validator
-    #end if
-    individual
-    #if str($study) != 'use_provided'
-      --study $study
-    #end if
-  </command>  
-
-  <inputs>
-    <param format="tabular" name="input" type="data"
-	   label="A tabular dataset with the following columns ..."/>
-    <param name="study" type="select" label="Context study" 
-	   help="Choose from the already defined studies. See below.">    
-      <options from_parameter="tool.app.known_studies" 
-	       transform_lines="[ &quot;%s%s%s:%s&quot; 
-                                  % ( l[0], self.separator, l[0], l[1][:40] ) 
-                                  for l in obj ]">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <filter type="sort_by" column="0"/>
-        <filter type="add_value" name="Records will provide study labels" 
-                value="use_provided" index="0"/>
-      </options>
-    </param>
-
-    <!-- ************************************************** -->
-    <param name="blocking_validation" type="boolean" checked="false"
-	   label="Blocking validation"
-	   help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/>
-
-     <conditional name="wait_for_trigger">
-      <param name="enable_trigger" type="boolean" checked="false"
-	     label="Wait for another tool to end before running this tool"/>
-      <when value="true">
-	<param format="txt" name="trigger_file" type="data"
-	       label="Select the LOG file that will be used as trigger"/>
-      </when>
-    </conditional>   
-
-    <conditional name="advanced_configuration">
-      <param name="configuration_level" type="select" 
-	     label="Configuration level">
-	<option value="default" selected="true">Default configuration</option>	
-	<option value="advanced">Advanced configuration</option>
-      </param>
-      <when value="default"/>
-      <when value="advanced">
-	<param name="vl_host" size="40" type="text" value="localhost" 
-	       label="Omero/VL host"/>
-	<param name="vl_user" size="20" type="text" value="root" 
-	       label="Omero/VL user"/>
-	<param name="vl_passwd" size="20" type="text" value="What?Me worry?" 
-	       label="Omero/VL passwd"/>
-      </when>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <data format="tabular" name="output" label="${tool.name}.mapping"/>
-    <data format="tabular" name="report" label="${tool.name}.report"/>
-    <data format="txt" name="logfile" label="${tool.name}.logfile"/>
-  </outputs>
-
-  <help>
-Will import a stream of new individual definitions defined by the
-following columns::
-
-  label gender   father mother
-  id2   male   id4    id5
-  id3   female None   None
-  ....
-
-It is not possible to import the same individual twice: the related
-file rows will be noisily ignored.
-  </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>
diff -r 8fdf5996c0fb -r 5ceb7668e259 boh/laneslot.xml
--- a/boh/laneslot.xml	Thu Sep 22 08:37:42 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,127 +0,0 @@
-<tool id="vl_import_laneslot" name="VLI.laneslot">
-  <description>import LaneSlot definitions within omero.biobank</description>
-  <command interpreter="python">
-    importer.py
-    #if $advanced_configuration.configuration_level == 'advanced'
-      --host=$advanced_configuration.vl_host
-      --user=$advanced_configuration.vl_user
-      --passwd=$advanced_configuration.vl_passwd
-    #end if
-    --operator=galaxy
-    --ifile=${in_file}
-    --ofile=${out_file}
-    --report_file=${report_file}
-    --loglevel=$__app__.config.vl_loglevel
-    --logfile=${log_file}
-    #if $blocking_validation
-      --blocking-validator
-    #end if
-    laneslot
-    #if str($study) != 'use_provided'
-      --study=${study}
-    #end if
-    #if str($source_type) != 'use_provided'
-      --source_type=${source_type}
-    #end if
-    #if str($content) != 'use_provided'
-      --content=${content}
-    #end if
-  </command>
-
-  <inputs>
-    <param format="tabular" name="in_file" type="data"
-	   label="A tabular dataset with the following columns..."/>
-
-    <param name="study" type="select" label="Context study"
-	   help="Choose from the already defined studies. See below.">
-      <options from_parameter="tool.app.known_studies"
-	       transform_lines="[ &quot;%s%s%s:%s&quot;
-	                          % ( l[0], self.separator, l[0], l[1][:40] )
-				  for l in obj ]">
-	<column name="value" index="0"/>
-	<column name="name" index="1"/>
-	<filter type="sort_by" column="0"/>
-	<filter type="add_value" name="Records provide study labels"
-		value="use_provided" index="0"/>
-      </options>
-    </param>
-
-    <param name="source_type" type="select"
-	   label="Type of the source object"
-	   help="Choose from the legal types. Seel below.">
-      <option value="use_provided" selected="true">
-	Records provide source type
-      </option>
-      <option value="Tube">Tube</option>
-      <option value="PlateWell">PlateWell</option>
-      <option value="Individual">Individual</option>
-    </param>
-
-    <param name="content" type="select"
-	   label="Type of content"
-	   help="Choose from the legal types. See below.">
-      <option value="use_provided" selected="true">
-	Records provide content type
-      </option>
-      <option value="DNA">DNA</option>
-      <option value="RNA">RNA</option>
-    </param>
-
-    <!-- ************************************************** -->
-    <param name="blocking_validation" type="boolean" checked="false"
-	   label="Blocking validation"
-	   help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/>
-
-    <conditional name="wait_for_trigger">
-      <param name="enable_trigger" type="boolean" checked="false"
-	     label="Wait for another tool to end before running this tool"/>
-      <when value="true">
-	<param format="txt" name="trigger_file" type="data"
-	       label="Select the LOG file that will be used as trigger"/>
-      </when>
-    </conditional>   
-
-    <conditional name="advanced_configuration">
-      <param name="configuration_level" type="select" 
-	     label="Configuration level">
-	<option value="default" selected="true">Default configuration</option>	
-	<option value="advanced">Advanced configuration</option>
-      </param>
-      <when value="default"/>
-      <when value="advanced">
-	<param name="vl_host" size="40" type="text" value="localhost" 
-	       label="Omero/VL host"/>
-	<param name="vl_user" size="20" type="text" value="root" 
-	       label="Omero/VL user"/>
-	<param name="vl_passwd" size="20" type="text" value="What? Me_worry?" 
-	       label="Omero/VL passwd"/>
-      </when>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <data format="tabular" name="out_file" label="${tool.name}.mapping"/>
-    <data format="tabular" name="report_file" label="${tool.name}.report"/>
-    <data format="txt" name="log_file" label="${tool.name}.logfile"/>
-  </outputs>
-
-  <help>
-A lane slot record will have the following fields::
-
-  lane     tag     content    source
-  V123411  ATCACG  DNA        V4512415
-  V123411  CGATGT  DNA        V1415512
-  V412511          DNA        V1909012
-  V661251  TGACCA  DNA        V1123111
-  V661251  CTTGTA  DNA        V1211141
-  ....
-
-the content column can be option if passed as script's input value,
-tag column is optional too.
-  </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>
\ No newline at end of file
diff -r 8fdf5996c0fb -r 5ceb7668e259 boh/marker_alignment.xml
--- a/boh/marker_alignment.xml	Thu Sep 22 08:37:42 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,140 +0,0 @@
-<tool id="vl_import_marker_alignment" name="VLI.marker_alignment">
-  <description>import marker aligments within omero/vl</description>
-  <command interpreter="python">
-    #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py
-    #else #unauthorized_access.py
-    #end if
-    #if $advanced_configuration.configuration_level == 'advanced'
-      --host=$advanced_configuration.vl_host
-      --user=$advanced_configuration.vl_user
-      --passwd=$advanced_configuration.vl_passwd
-    #end if
-    --operator=galaxy
-    --ifile=$input
-    --report_file=$report
-    --loglevel=$__app__.config.vl_loglevel
-    --logfile=${logfile}
-    marker_alignment
-    #if str($study) != 'use_provided'
-      --study ${study}
-    #end if 
-    #if str($ref_genome)
-      --ref-genome ${reg_genome}
-    #end if 
-    #if str($message)
-      --message ${message}
-    #end if 
-  </command>  
-
-  <inputs>
-    <!-- use a special format to automatically pick up the ref-gen -->
-    <param format="tabular" name="input" type="data"
-	   label="A tabular dataset with the following columns ..."/>
-
-    <param name="study" type="select" label="Context study" 
-	   help="Choose from the already defined studies. See help below.">    
-      <options from_parameter="tool.app.known_studies" 
-	       transform_lines="[ &quot;%s%s%s:%s&quot; 
-                                  % ( l[0], self.separator, l[0], l[1][:40] ) 
-                                  for l in obj ]">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <filter type="sort_by" column="0"/>
-        <filter type="add_value" name="Records provide study labels" 
-                value="use_provided" index="0"/>
-      </options>
-    </param>
-
-    <conditional name="genomeSource">
-      <param name="refGenomeSource"
-	     type="select" 
-	     label="Will you select a reference genome from your history 
-                   or use a built-in index?">
-        <option value="indexed">Use a built-in index</option>
-        <option value="history">Use one from the history</option>
-      </param>
-      <when value="indexed">
-        <param name="indices" type="select" label="Select a reference genome">
-          <options from_data_table="libbwa_indexes">
-            <filter type="sort_by" column="2" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ownFile" type="data" 
-	       format="fasta" metadata_name="dbkey" 
-	       label="Select a reference from history" />
-      </when>
-    </conditional>
-    <conditional name="paired">
-      <param name="sPaired" type="select" label="Is this library mate-paired?">
-        <option value="single">Single-end</option>
-        <option value="paired">Paired-end</option>
-      </param>
-      <when value="single">
-        <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" />
-      </when>
-      <when value="paired">
-        <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" />
-        <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" />
-      </when>
-    </conditional>
-
-    <param name="source" size="40" type="text" value="" 
-	   label="source"/>
-    <param name="context" size="40" type="text" value="" 
-	   label="context"/>
-    <param name="release" size="40" type="text" value="" 
-	   label="release"/>
-
-
-    <!-- ************************************************** -->
-    <conditional name="advanced_configuration">
-      <param name="configuration_level" type="select" 
-	     label="Configuration level">
-	<option value="default" selected="true">Default configuration</option>	
-	<option value="advanced">Advanced configuration</option>
-      </param>
-      <when value="default"/>
-      <when value="advanced">
-	<param name="vl_host" size="40" type="text" value="localhost" 
-	       label="Omero/VL host"/>
-	<param name="vl_user" size="20" type="text" value="root" 
-	       label="Omero/VL user"/>
-	<param name="vl_passwd" size="20" type="text" value="What?Me worry?" 
-	       label="Omero/VL passwd"/>
-      </when>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <data format="tabular" name="report" label="${tool.name}.report"/>
-    <data format="txt" name="logfile" label="${tool.name}.logfile"/>
-  </outputs>
-
-  <help>
-Will read in a tsv file with the following columns::
-
-  marker_vid ref_genome chromosome pos      strand allele copies
-  V0909090   hg18       10         82938938 True   A      1
-  V0909091   hg18       1          82938999 True   A      2
-  V0909092   hg18       1          82938938 True   B      2
-  ...
-
-Since pos is relative to 5', if the marker has been aligned on the
-other strand, it is the responsibility of the aligner app to report
-the actual distance from 5', while, at the same time, registering that
-the SNP has actually been aligned on the other strand.
-
-The chromosome field is an integer field with values in the [1, 26]
-range, with 23-26 representing, respectively, the X chromosome, the Y
-chromosome, the pseudoautosomal regions (XY) and the mitochondrial DNA
-(MT).
- </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>
diff -r 8fdf5996c0fb -r 5ceb7668e259 boh/marker_definition.xml
--- a/boh/marker_definition.xml	Thu Sep 22 08:37:42 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,119 +0,0 @@
-<tool id="vl_import_marker_definition" name="VLI.marker_definition">
-  <description>import Marker definitions within omero/vl</description>
-  <command interpreter="python">
-    #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py
-    #else #unauthorized_access.py
-    #end if
-    #if $advanced_configuration.configuration_level == 'advanced'
-      --host=$advanced_configuration.vl_host
-      --user=$advanced_configuration.vl_user
-      --passwd=$advanced_configuration.vl_passwd
-    #end if
-    --operator=galaxy
-    --ifile=$input1
-    --ofile=$output1
-    --loglevel=$__app__.config.vl_loglevel
-    --logfile=${logfile}
-    marker_definition
-    #if str($study) != 'use_provided'
-      --study ${study}
-    #end if 
-    --source ${source}
-    --context ${context}
-    --release ${release}
-    --ref-genome  ${ref_genome}
-    --dbsnp-build ${dbsnp_build}
-  </command>  
-
-  <inputs>
-    <param format="tabular" name="input1" type="data"
-	   label="A tabular dataset with the following columns ..."/>
-
-    <param name="study" type="select" label="Context study" 
-	   help="Choose from the already defined studies. See help below.">    
-      <options from_parameter="tool.app.known_studies" 
-	       transform_lines="[ &quot;%s%s%s:%s&quot; 
-                                  % ( l[0], self.separator, l[0], l[1][:40] ) 
-                                  for l in obj ]">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <filter type="sort_by" column="0"/>
-        <filter type="add_value" name="Records provide study labels" 
-                value="use_provided" index="0"/>
-      </options>
-    </param>
-
-    <param name="source" size="40" type="text" value="" 
-	   optional="false"
-	   label="source"/>
-    <param name="context" size="40" type="text" value="" 
-	   optional="false"
-	   label="context"/>
-    <param name="release" size="40" type="text" value="" 
-	   optional="false"
-	   label="release"/>
-    <param name="ref_genome" size="40" type="text" value="" 
-	   optional="false"
-	   label="reference genome"/>
-    <param name="dbsnp_build" size="40" type="integer" value="0"
-	   optional="false"
-	   label="dbSNP build"/>
-
-
-    <!-- ************************************************** -->
-    <conditional name="advanced_configuration">
-      <param name="configuration_level" type="select" 
-	     label="Configuration level">
-	<option value="default" selected="true">Default configuration</option>	
-	<option value="advanced">Advanced configuration</option>
-      </param>
-      <when value="default"/>
-      <when value="advanced">
-	<param name="vl_host" size="40" type="text" value="localhost" 
-	       label="Omero/VL host"/>
-	<param name="vl_user" size="20" type="text" value="root" 
-	       label="Omero/VL user"/>
-	<param name="vl_passwd" size="20" type="text" value="What?Me worry?" 
-	       label="Omero/VL passwd"/>
-      </when>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <data format="tabular" name="output1" label="${tool.name}.mapping"/>
-    <data format="txt" name="logfile"     label="${tool.name}.logfile"/>
-  </outputs>
-
-  <help>
-Will read in a tsv file with the following columns::
-
-  label         rs_label   mask                    strand allele_a allele_b
-  SNP_A-1780419 rs6576700  <lflank/>[A/G]<rflank/> TOP    A      G
-  ...
-
-Where label is supposed to be the unique label for this marker in the
-(source, context, release) context, rs_label is the dbSNP db label for
-this snp (it could be the string ``None`` if not defined or not
-known). The column mask contains the SNP definition. The strand column
-could either be the actual 'illumina style' strand used to define the
-alleles in the alleles columns, or the string 'None', which means that
-the alleles in the allele column are defined wrt the mask in the
-mask column.
-
-It will, for each row, convert the mask to the TOP strand following
-Illumina conventions and then save a record for it in VL. The saved
-tuple is (source, context, release, label, rs_label, TOP_mask). There
-are no collision controls.
-
-It will output a a tsv file with the following columns::
-
-   study    label     type    vid
-   ASTUDY   SNP_A-xxx Marker  V000002222
-   ...
- </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>